GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Pseudomonas fluorescens FW300-N1B4

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Pf1N1B4_1382 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1382
          Length = 377

 Score =  279 bits (714), Expect = 8e-80
 Identities = 150/359 (41%), Positives = 212/359 (59%), Gaps = 5/359 (1%)

Query: 12  FAAMAIAGFASYSMAADT-IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAGGVNGAQ 70
           F A+A+A     S  A   IKI +AGP+TG  A +G+    GA  A + +N AGGVNG +
Sbjct: 10  FLALAVATALGVSAFAQADIKIGVAGPMTGANAAFGEQYMKGAQAAADAVNAAGGVNGEK 69

Query: 71  LEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSATA 130
           +  V  DDAC+PKQAV VA  + N  V  VVGH CSSST PA++IY++ G++ ITP +T 
Sbjct: 70  IVLVKGDDACEPKQAVTVAKDLTNQKVAGVVGHFCSSSTIPASEIYDEAGIIAITPGSTN 129

Query: 131 PEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKTVE 190
           P +T RG   +FR  G D+ QG VAG +I +  K K + VLHDK  YG+G+A   K  + 
Sbjct: 130 PAVTERGLSAMFRMCGRDDQQGIVAGDYIVDVLKGKKVVVLHDKDTYGQGLADATKAQLA 189

Query: 191 DAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGL-DARF 249
             G+   ++EGL  G+KDF+ +++K++ AG   VYFGG HPE G L+RQ ++ GL D +F
Sbjct: 190 KRGVTPVLYEGLTRGEKDFSTIVTKIRGAGADVVYFGGLHPEAGPLVRQLREQGLKDVKF 249

Query: 250 MGPEGVGNSEITAIAGDAS--EGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVLPA 307
           M  +G+   E+   AG     +G+L T        P +K ++D F+ K  +P G + L A
Sbjct: 250 MSDDGIVTDELVTTAGGPQFVDGVLMTFGADPRLLPDSKTVVDDFRKKGTEPEG-YTLYA 308

Query: 308 YSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEWHKD 366
           Y++V  +A     A     E+ A  L+ N  +T  G   +D KGDLK  D+ VY+W KD
Sbjct: 309 YASVQTLAAAFNGAKSNKGEEAAAWLKKNPVKTVMGEKTWDSKGDLKISDYVVYQWDKD 367


Lambda     K      H
   0.316    0.133    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 402
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 373
Length of database: 377
Length adjustment: 30
Effective length of query: 343
Effective length of database: 347
Effective search space:   119021
Effective search space used:   119021
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory